UCSF-Chimera/C2/Structure-Manipulation/English-timed
From Script | Spoken-Tutorial
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| 00:01 | Welcome to this tutorial on Structure Manipulation using Chimera. |
| 00:06 | In this tutorial, we will learn to: open a structure on the Chimera window, |
| 00:12 | move, rotate and zoom the structure, scale and clip, and change the display of the structure. |
| 00:20 | To follow this tutorial, you should have knowledge of undergraduate Biochemistry or
must be familiar with Structural Biology. |
| 00:29 | To record this tutorial, I am using: Ubuntu Linux OS version. 14.04, Chimera version 1.10.2,
Mozilla Firefox browser 35.0 and a working internet connection. |
| 00:47 | UCSF Chimera is a software for interactive visualization and analysis of molecular structures. |
| 00:55 | Chimera is developed by the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco. |
| 01:05 | More information is available at the given link. |
| 01:09 | To start the Chimera window, click or double-click on the Chimera icon present on the desktop. |
| 01:16 | A Rapid access interface opens. |
| 01:20 | Rapid access window allows you to access the frequently used data and tools. |
| 01:27 | Click the lightning bolt icon at the bottom right corner of the window. |
| 01:32 | This will display the graphics window. 3D structures and other data are displayed on this window. |
| 01:40 | Toggle between the two windows by clicking the lightning bolt icon. |
| 01:45 | Let me now go back to graphics window. |
| 01:48 | Many tasks in Chimera can be accomplished by two methods. |
| 01:53 | First one, by making use of menu bar, located at the top of the Chimera window. |
| 01:59 | Other is by entering commands on the command line. |
| 02:03 | To show the command line, click on Favorites menu. |
| 02:06 | Scroll down and click on command line option. |
| 02:10 | A command dialog box appears at the bottom of the Chimera window. |
| 02:15 | Commands for a particular task are to be written in the text box. |
| 02:21 | We will learn more about this feature in the subsequent tutorials. |
| 02:25 | To resize the window, drag any corner of the window. |
| 02:30 | Now, let us see how to open a protein structure. |
| 02:34 | There are 3 ways you can do it. If you are connected to Internet, click on the File menu. |
| 02:40 | Scroll down and click on “Fetch by ID” option. |
| 02:45 | A dialog box appears on the screen. |
| 02:48 | You can connect to various databases to fetch the structure. |
| 02:53 | For demonstration, I wish to display a protein structure. |
| 02:58 | I will select PDB from the options. Type the 4 letter PDB code of the protein molecule you intend to display. |
| 03:08 | I will type 1zik (one z i k). |
| 03:12 | This is the pdb code for Leucine zipper protein. Click on Fetch button. |
| 03:19 | By default, a ribbons display of the protein will appear on the display window. |
| 03:25 | We can also type a command to fetch a structure. |
| 03:29 | In the command line text box, type “open 1zik”. |
| 03:35 | Press Enter to open the structure on the display window. |
| 03:40 | If you are not connected to internet, you can open the already downloaded pdb file. |
| 03:46 | To clear the structure present on the screen: scroll down the Favorites menu and click on Model Panel option. |
| 03:55 | A Model Panel dialog box opens. |
| 03:58 | Click on model id, then click on Close option. |
| 04:04 | Close the model panel window. |
| 04:07 | Now I will demonstrate how to download a PDB file. |
| 04:12 | You need a working internet connection to download the pdb file. |
| 04:17 | Scroll down the File menu and click on Fetch by ID option. |
| 04:23 | A dialog box opens. |
| 04:26 | Scroll down to bottom of the dialog box. |
| 04:30 | Click on web page button. |
| 04:33 | PDB database web page opens in the browser. |
| 04:37 | If you know the pdb code for the protein, type in the text box provided. Or, type the name of the protein. |
| 04:46 | I know the pdb code for leucine zipper. So, I will type “1zik” in the text box. |
| 04:54 | Click on Go button. |
| 04:57 | Scroll down the page. |
| 04:59 | Click on the Download files button located on the right-hand corner of the page. |
| 05:06 | From the drop-down menu click on PDB-file-text option. |
| 05:12 | A dialog box appears. |
| 05:14 | Click on Save File option. |
| 05:17 | Click on Ok button. |
| 05:20 | The downloaded pdb file will now be saved in the Downloads folder. |
| 05:25 | Back to the Chimera window. |
| 05:27 | Close the dialog box. |
| 05:30 | To open the already downloaded pdb file, click on Open option in File. |
| 05:37 | Navigate to the Downloads folder. Select 1zik.pdb file. |
| 05:44 | Click on “Open” button. |
| 05:47 | A model of leucine zipper is displayed on the panel. |
| 05:51 | By default, the two peptide chains are displayed as grey ribbons. |
| 05:57 | Use the mouse button to move the structure on the panel. |
| 06:01 | Left mouse button for rotation, |
| 06:04 | the middle mouse button controls xy translation. |
| 06:08 | The right button or the mouse wheel to zoom in or zoom out. |
| 06:13 | For interactive scaling and clipping of the structure: use Side View option from Favorites menu. |
| 06:20 | A viewing window opens. |
| 06:22 | A tiny version of the structure is shown on the window. |
| 06:27 | The yellow square on the left, represents the viewer's eye position |
| 06:32 | Try moving the small square using left mouse button. |
| 06:36 | Dragging it horizontally, adjust the scale factor. |
| 06:41 | Double-clicking the eye position shows a menu for changing the camera mode. |
| 06:46 | Move the clipping planes i.e. the two vertical lines using left mouse button. |
| 06:53 | There are more viewing controls on the window which you can explore. |
| 06:58 | Close the viewing window. |
| 07:01 | Let us now learn to manipulate this structure. |
| 07:04 | The first step is to select the part of the structure you want to modify. |
| 07:09 | For now, I want to show the entire protein structure as atoms. |
| 07:15 | Click on the Select menu in the menu bar. |
| 07:19 | Select menu in the menu bar will allow us to select individual components of the structure |
| 07:25 | such as chain, element, residue, ligand etc. |
| 07:31 | However, if nothing is selected from the “Select” menu, it means we want to modify the entire structure. |
| 07:39 | Now go to Actions menu, and select atoms/bonds from the options. |
| 07:46 | Click on show from the sub-menu. |
| 07:49 | On the screen, we see atoms as well as part of the structure as ribbons. |
| 07:55 | Now to remove ribbons, select ribbons from the Action menu. |
| 08:00 | Then click on hide option. |
| 08:03 | The entire structure is now shown as sticks display. |
| 08:08 | Let us now proceed with a bit more manipulation of the structure. |
| 08:13 | The following steps will convert it to the ball and stick display. |
| 08:18 | Click on Actions menu. |
| 08:21 | Scroll down to atoms/bonds. |
| 08:24 | Select ball and stick from the sub-menu. |
| 08:28 | Notice that the structure is without hydrogen atoms. |
| 08:33 | To add hydrogen atoms, scroll down the Tools menu. |
| 08:37 | Click on Structure Editing. |
| 08:40 | From the sub-menu, select Add hydrogens option. |
| 08:45 | In the dialog box, make selections as shown. |
| 08:49 | Click on OK button. |
| 08:52 | Observe that the structure is now shown with hydrogen atoms. |
| 08:57 | Usually the structure of a protein is associated with water molecules. |
| 09:02 | To hide water molecules, go to Select menu, scroll down to Residue, click on HOH option. |
| 09:13 | Observe the screen; all the water molecules are highlighted. |
| 09:18 | Go to actions menu, scroll down to Atoms\bonds and click on hide option. |
| 09:26 | This will hide the water molecules from the structure. |
| 09:30 | The Presets option in the menu bar has some more options to change the display. |
| 09:36 | When you click on Interactive 1 option: the structure will be displayed as ribbons and both the peptide chains in different color. |
| 09:45 | Interactive 2 will convert the structure to atoms display. |
| 09:50 | Go back to Interactive 1 display. |
| 09:53 | We can also selectively change the color of peptide chains. |
| 09:57 | Scroll down the Select menu and select chain A from the sub-menu. |
| 10:02 | Chain A is now highlighted. |
| 10:05 | Go to Actions menu scroll down to color, select yellow. |
| 10:11 | Chain A is now displayed in yellow color. |
| 10:15 | To clear the selection, hold CTRL key on the key board. And click on the empty space on the Chimera window. |
| 10:23 | We have now come to the end of this tutorial. |
| 10:26 | To exit the Chimera window, go to File menu and click on Quit option. |
| 10:32 | Let's summarize. In this tutorial, we have learnt to" open a structure on the Chimera window and download the PDB file for protein structures, |
| 10:43 | move, rotate and zoom the structure, Scale and clip, |
| 10:49 | change the display using menus in the menu bar, |
| 10:53 | remove the water molecules, and add hydrogens. |
| 10:57 | For the Assignment, download the pdb file of Leucine zipper from PDB database. |
| 11:04 | Open the pdb file on Chimera window using Open option in the File menu. |
| 11:10 | Change the display of atoms to wire and all the aromatic rings as disks. |
| 11:16 | Your completed assignment will look as follows. |
| 11:21 | The video at the following link summarizes the Spoken Tutorial project. |
| 11:26 | Please download and watch it. |
| 11:28 | The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test. |
| 11:34 | For more details, please write to us. |
| 11:38 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. |
| 11:44 | More information on this mission is available at the link shown. |
| 11:48 | This is Snehalatha from IIT Bombay, signing off.
Thank you for joining. |
